Data mining of flax transcriptome profile under stress aluminum toxicity and zinc deficiency

Flax (Linum usitatissimum L.) is cultivated all over the world on a large scale due to its wide use in the food, textile, and pharmaceutical industries. One of the factors that affect the cultivation of this plant is abiotic stresses, such as inappropriate pH and soil with a lack or toxicity of nutrients, which leads to a decrease in its quantity and quality. Therefore, it is necessary to identify genes responsive to different stresses. In the present study, using RNA-Seq data obtained from the roots of flax plants under the stress of aluminum toxicity and zinc deficiency, DEGs were investigated to identify stress-responsive changes in two resistant and sensitive cultivars. In total, 30 common DEGs were identified between resistant cultivars and 97 common DEGs between sensitive cultivars in both stresses in which, the number of DEGs was more in the sensitive cultivar and four genes were common between sensitive and resistant cultivars. The most general changes of common DEGs were related to flax-specific biological processes, metabolic processes, and cellular processes, which indicate the metabolically active state of the plant cell. Resistant cultivars responded more specifically and most of the genes were grouped in GO related to response to stimuli. In the protein-protein interaction network of susceptible cultivars, chitinases and the PR4 gene had the most related to other proteins, while in the resistant cultivars, the resistance strategy was different, and the expression of cell wall modifying genes showed the highest relation with other proteins. In general, the expression profile of stress-responsive genes showed that the PR1 gene had the most changes in both cultivars and can be used as a resistance marker for plant breeding purposes. Also, the biosynthesis of secondary metabolites, which is a response to stress, increased significantly. The obtained results provide new insights into the mechanism of tolerance to abiotic stress in flax, which can be used to improve the quantitative and qualitative yields.